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Testing of multiple rsLTL formulae at once

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This commit is contained in:
Artur Meski
2017-11-05 17:53:08 +00:00
parent a9a37baba7
commit 4dbeac742d
1 changed files with 207 additions and 109 deletions
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316
smt/smt_checker_rsc_param.py
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@@ -37,14 +37,24 @@ class SmtCheckerRSCParam(object):
def initialise(self):
"""Initialises all the variables used by the checker"""
self.v = []
self.v_ctx = []
self.ca_state = []
### "Currently" used variables (loaded from self.path_v...)
self.v = None
self.v_ctx = None
self.ca_state = None
# intermediate products:
self.v_improd = []
self.v_improd_for_entities = []
self.v_improd = None
self.v_improd_for_entities = None
### Per-path variables
self.path_v = dict()
self.path_v_ctx = dict()
self.path_ca_state = dict()
# intermediate products:
self.path_v_improd = dict()
self.path_v_improd_for_entities = dict()
# parameters:
self.v_param = dict()
@@ -60,9 +70,11 @@ class SmtCheckerRSCParam(object):
# improd - intermediate products
# improducible - entities that are never produces (there is no reaction that produces that entity)
self.loop_position = Int("loop_position")
# TODO: number of loops == number of paths
self.loop_position = None
self.path_loop_position = dict()
if self.optimise:
if self.optimise:
self.solver = Optimize()
else:
self.solver = Solver() #For("QF_FD")
@@ -74,40 +86,67 @@ class SmtCheckerRSCParam(object):
def reset(self):
"""Reinitialises the state of the checker"""
self.initialise()
self.initialise()
def prepare_all_variables(self):
"""Prepares all the variables"""
def prepare_all_variables(self, num_of_paths):
self.prepare_state_variables()
self.prepare_context_variables()
self.prepare_intermediate_product_variables()
self.next_level_to_encode += 1
for path_idx in range(num_of_paths):
self.prepare_all_path_variables(path_idx)
self.next_level_to_encode += 1
def prepare_context_variables(self):
def prepare_all_path_variables(self, path_idx):
"""Prepares the variables for a given path index"""
print_info("Preparing variables for path={:d} (level={:d})".format(path_idx, self.next_level_to_encode))
self.prepare_state_variables(path_idx)
self.prepare_context_variables(path_idx)
self.prepare_intermediate_product_variables(path_idx)
self.prepare_loop_position_variables(path_idx)
def prepare_loop_position_variables(self, path_idx):
"""Prepares the variables for loop positions"""
self.path_loop_position[path_idx] = Int("p{:d}_loop_pos".format(path_idx))
def prepare_context_variables(self, path_idx):
"""Prepares all the context variables"""
level = self.next_level_to_encode
self.path_v_ctx.setdefault(path_idx, [])
assert len(self.path_v_ctx[path_idx]) == level
variables = []
for entity in self.rs.background_set:
variables.append(Int("C"+str(level)+"_"+entity))
new_var = Int("p{:d}C{:d}_{:s}".format(path_idx, level, entity))
variables.append(new_var)
self.v_ctx.append(variables)
self.path_v_ctx[path_idx].append(variables)
def prepare_state_variables(self):
def prepare_state_variables(self, path_idx):
"""Prepares all the state variables"""
level = self.next_level_to_encode
# RS vars
self.path_v.setdefault(path_idx, [])
assert len(self.path_v[path_idx]) == level
variables = []
for entity in self.rs.background_set:
variables.append(Int("L"+str(level)+"_"+entity))
self.v.append(variables)
new_var = Int("p{:d}L{:d}_{:s}".format(path_idx, level, entity))
variables.append(new_var)
self.path_v[path_idx].append(variables)
self.ca_state.append(Int("CA"+str(level)+"_state"))
# Context automaton states:
self.path_ca_state.setdefault(path_idx, [])
assert len(self.path_ca_state[path_idx]) == level
ca_state_var = Int("p{:d}CA{:d}_state".format(path_idx, level))
self.path_ca_state[path_idx].append(ca_state_var)
def prepare_intermediate_product_variables(self):
def prepare_intermediate_product_variables(self, path_idx):
"""
Prepares the intermediate product variables
carrying the individual concentration levels produced
@@ -119,14 +158,20 @@ class SmtCheckerRSCParam(object):
level = self.next_level_to_encode
self.path_v_improd.setdefault(path_idx, [])
self.path_v_improd_for_entities.setdefault(path_idx, [])
assert len(self.path_v_improd[path_idx]) == level
assert len(self.path_v_improd_for_entities[path_idx]) == level
if level < 1:
#
# If we are at level==0, we add a dummy "level"
# to match the indices of of the successors
# which are always at level+1.
#
self.v_improd.append(None)
self.v_improd_for_entities.append(None)
self.path_v_improd[path_idx].append(None)
self.path_v_improd_for_entities[path_idx].append(None)
else:
reactions_dict = dict()
@@ -145,8 +190,7 @@ class SmtCheckerRSCParam(object):
for entity in self.rs.set_of_bgset_ids:
entity_name = self.rs.get_entity_name(entity)
new_var = Int("L"+ str(level) + "_ImProd" + "_r" +
str(reaction_id) + "_" + entity_name)
new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
entities_dict[entity] = new_var
all_entities_dict.setdefault(entity, [])
@@ -156,8 +200,7 @@ class SmtCheckerRSCParam(object):
for entity, conc in products:
entity_name = self.rs.get_entity_name(entity)
new_var = Int("L"+ str(level) + "_ImProd" + "_r" +
str(reaction_id) + "_" + entity_name)
new_var = Int("p{:d}L{:d}_ImProd_r{:d}_{:s}".format(path_idx, level, reaction_id, entity_name))
entities_dict[entity] = new_var
all_entities_dict.setdefault(entity, [])
@@ -165,8 +208,8 @@ class SmtCheckerRSCParam(object):
reactions_dict[reaction_id] = entities_dict
self.v_improd.append(reactions_dict)
self.v_improd_for_entities.append(all_entities_dict)
self.path_v_improd[path_idx].append(reactions_dict)
self.path_v_improd_for_entities[path_idx].append(all_entities_dict)
def prepare_param_variables(self):
"""
@@ -187,6 +230,17 @@ class SmtCheckerRSCParam(object):
vars_for_param.append(new_var)
self.v_param[param_name] = vars_for_param
def load_varset_for_path(self, path_idx):
"""
Loads the the variables for the path with path_idx
"""
self.v = self.path_v[path_idx]
self.v_ctx = self.path_v_ctx[path_idx]
self.ca_state = self.path_ca_state[path_idx]
self.v_improd = self.path_v_improd[path_idx]
self.v_improd_for_entities = self.path_v_improd_for_entities[path_idx]
self.loop_position = self.path_loop_position[path_idx]
def enc_param_concentration_levels_assertion(self):
"""
@@ -218,50 +272,52 @@ class SmtCheckerRSCParam(object):
for pvar in param_vars:
self.solver.add_soft(pvar < 1)
def enc_concentration_levels_assertion(self, level):
def enc_concentration_levels_assertion(self, level, path_idx):
"""
Encodes assertions that (some) variables need to be >=0
We do not need to actually control all the variables,
only those that can possibly go below 0.
"""
print_info("Concentration level assertions for path={:d} (level={:d})".format(path_idx, level))
enc_gz = True
for e_i in self.rs.set_of_bgset_ids:
var = self.v[level][e_i]
var_ctx = self.v_ctx[level][e_i]
var = self.path_v[path_idx][level][e_i]
var_ctx = self.path_v_ctx[path_idx][level][e_i]
e_max = self.rs.get_max_concentration_level(e_i)
enc_gz = simplify(And(enc_gz, var >= 0, var_ctx >= 0, var <= e_max, var_ctx <= e_max))
vars_per_reaction = self.v_improd_for_entities[level + 1]
vars_per_reaction = self.path_v_improd_for_entities[path_idx][level + 1]
if e_i in vars_per_reaction:
for var_improd in vars_per_reaction[e_i]:
enc_gz = simplify(And(enc_gz, var_improd >= 0, var_improd <= e_max))
return enc_gz
def enc_init_state(self, level):
def enc_init_state(self, level, path_idx):
"""Encodes the initial state at the given level"""
rs_init_state_enc = True
for v in self.v[level]:
for v in self.path_v[path_idx][level]:
# the initial concentration levels are zeroed
rs_init_state_enc = simplify(And(rs_init_state_enc, v == 0))
ca_init_state_enc = self.ca_state[level] == self.ca.get_init_state_id()
ca_init_state_enc = self.path_ca_state[path_idx][level] == self.ca.get_init_state_id()
init_state_enc = simplify(And(rs_init_state_enc, ca_init_state_enc))
return init_state_enc
def enc_transition_relation(self, level):
def enc_transition_relation(self, level, path_idx):
return simplify(
And(self.enc_rs_trans(level),
self.enc_automaton_trans(level)))
And(self.enc_rs_trans(level, path_idx),
self.enc_automaton_trans(level, path_idx)))
def enc_single_reaction(self, level, reaction):
def enc_single_reaction(self, level, path_idx, reaction):
"""
Encodes a single reaction
@@ -285,13 +341,13 @@ class SmtCheckerRSCParam(object):
for entity in self.rs.set_of_bgset_ids:
enc_reactants = And(enc_reactants, Or(
self.v_param[param_name][entity] == 0,
self.v[level][entity] >= self.v_param[param_name][entity],
self.v_ctx[level][entity] >= self.v_param[param_name][entity]))
self.path_v[path_idx][level][entity] >= self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity] >= self.v_param[param_name][entity]))
else:
for entity, conc in reactants:
enc_reactants = And(enc_reactants, Or(
self.v[level][entity] >= conc,
self.v_ctx[level][entity] >= conc))
self.path_v[path_idx][level][entity] >= conc,
self.path_v_ctx[path_idx][level][entity] >= conc))
# ** INHIBITORS ******************************************
enc_inhibitors = True
@@ -301,13 +357,13 @@ class SmtCheckerRSCParam(object):
enc_inhibitors = And(enc_inhibitors, Or(
self.v_param[param_name][entity] == 0,
And(
self.v[level][entity] < self.v_param[param_name][entity],
self.v_ctx[level][entity] < self.v_param[param_name][entity])))
self.path_v[path_idx][level][entity] < self.v_param[param_name][entity],
self.path_v_ctx[path_idx][level][entity] < self.v_param[param_name][entity])))
else:
for entity, conc in inhibitors:
enc_inhibitors = And(enc_inhibitors, And(
self.v[level][entity] < conc,
self.v_ctx[level][entity] < conc))
self.path_v[path_idx][level][entity] < conc,
self.path_v_ctx[path_idx][level][entity] < conc))
# ** PRODUCTS *******************************************
enc_products = True
@@ -315,22 +371,22 @@ class SmtCheckerRSCParam(object):
param_name = products.name
for entity in self.rs.set_of_bgset_ids:
enc_products = simplify(And(enc_products,
self.v_improd[level + 1][reaction_id][entity] == self.v_param[param_name][entity]))
self.path_v_improd[path_idx][level + 1][reaction_id][entity] == self.v_param[param_name][entity]))
else:
for entity, conc in products:
enc_products = simplify(And(enc_products,
self.v_improd[level + 1][reaction_id][entity] == conc))
self.path_v_improd[path_idx][level + 1][reaction_id][entity] == conc))
# Nothing is produced (when the reaction is disabled)
enc_no_prod = True
if is_param(products):
for entity in self.rs.set_of_bgset_ids:
enc_no_prod = And(enc_no_prod,
self.v_improd[level + 1][reaction_id][entity] == 0)
self.path_v_improd[path_idx][level + 1][reaction_id][entity] == 0)
else:
for entity, _ in products:
enc_no_prod = simplify(And(enc_no_prod,
self.v_improd[level + 1][reaction_id][entity] == 0))
self.path_v_improd[path_idx][level + 1][reaction_id][entity] == 0))
#
# (R and I) iff P
@@ -346,7 +402,7 @@ class SmtCheckerRSCParam(object):
return enc_reaction
def enc_general_reaction_enabledness(self, level):
def enc_general_reaction_enabledness(self, level, path_idx):
"""
General enabledness condition for reactions
@@ -362,11 +418,11 @@ class SmtCheckerRSCParam(object):
enc_cond = False
for entity in self.rs.set_of_bgset_ids:
enc_cond = simplify(Or(enc_cond, self.v[level][entity] > 0, self.v_ctx[level][entity] > 0))
enc_cond = simplify(Or(enc_cond, self.path_v[path_idx][level][entity] > 0, self.path_v_ctx[path_idx][level][entity] > 0))
return enc_cond
def enc_rs_trans(self, level):
def enc_rs_trans(self, level, path_idx):
"""Encodes the transition relation"""
#
@@ -386,7 +442,7 @@ class SmtCheckerRSCParam(object):
enc_trans = True
for reaction in self.rs.reactions:
enc_reaction = self.enc_single_reaction(level, reaction)
enc_reaction = self.enc_single_reaction(level, path_idx, reaction)
enc_trans = simplify(And(enc_trans, enc_reaction))
# Next we encode the MAX concentration values:
@@ -404,14 +460,14 @@ class SmtCheckerRSCParam(object):
# =>
# {products}[level+1]
#
current_v_improd_for_entities = self.v_improd_for_entities[level + 1]
current_v_improd_for_entities = self.path_v_improd_for_entities[path_idx][level + 1]
for entity in self.rs.set_of_bgset_ids:
per_reaction_vars = current_v_improd_for_entities.get(entity, [])
enc_max_prod = simplify(
And(enc_max_prod, self.v[level + 1][entity] == self.enc_max(per_reaction_vars)))
And(enc_max_prod, self.path_v[path_idx][level + 1][entity] == self.enc_max(per_reaction_vars)))
# make sure at least one entity is >0
enc_general_cond = self.enc_general_reaction_enabledness(level)
enc_general_cond = self.enc_general_reaction_enabledness(level, path_idx)
enc_trans_with_max = simplify(And(enc_general_cond, enc_max_prod, enc_trans))
@@ -437,14 +493,14 @@ class SmtCheckerRSCParam(object):
return enc
def enc_automaton_trans(self, level):
def enc_automaton_trans(self, level, path_idx):
"""Encodes the transition relation for the context automaton"""
enc_trans = False
for src,ctx,dst in self.ca.transitions:
src_enc = self.ca_state[level] == src
dst_enc = self.ca_state[level+1] == dst
src_enc = self.path_ca_state[path_idx][level] == src
dst_enc = self.path_ca_state[path_idx][level+1] == dst
all_ent = set(range(len(self.rs.background_set)))
@@ -454,10 +510,10 @@ class SmtCheckerRSCParam(object):
ctx_enc = True
for e,c in ctx:
ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == c))
ctx_enc = simplify(And(ctx_enc, self.path_v_ctx[path_idx][level][e] == c))
for e in excl_ctx:
ctx_enc = simplify(And(ctx_enc, self.v_ctx[level][e] == 0))
ctx_enc = simplify(And(ctx_enc, self.path_v_ctx[path_idx][level][e] == 0))
cur_trans = simplify(And(src_enc, ctx_enc, dst_enc))
enc_trans = simplify(Or(enc_trans, cur_trans))
@@ -500,7 +556,7 @@ class SmtCheckerRSCParam(object):
return simplify(enc)
def decode_witness(self, max_level, print_model=False):
def decode_witness(self, max_level, path_idx, print_model=False):
"""
Decodes the witness
@@ -517,8 +573,8 @@ class SmtCheckerRSCParam(object):
print("\n{: >70}".format("[ level=" + repr(level) + " ]"))
print(" State: {", end=""),
for var_id in range(len(self.v[level])):
var_rep = repr(m[self.v[level][var_id]])
for var_id in range(len(self.path_v[path_idx][level])):
var_rep = repr(m[self.path_v[path_idx][level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
@@ -532,8 +588,8 @@ class SmtCheckerRSCParam(object):
if level != max_level:
print(" Context set: ", end="")
print("{", end="")
for var_id in range(len(self.v[level])):
var_rep = repr(m[self.v_ctx[level][var_id]])
for var_id in range(len(self.path_v[path_idx][level])):
var_rep = repr(m[self.path_v_ctx[path_idx][level][var_id]])
if not var_rep.isdigit():
raise RuntimeError(
"unexpected: representation is not a positive integer")
@@ -566,7 +622,7 @@ class SmtCheckerRSCParam(object):
print("\n")
def check_rsltl(
self, formula,
self, formulae_list,
print_witness=True,
print_time=True, print_mem=True,
max_level=None, cont_if_sat=False):
@@ -582,81 +638,123 @@ class SmtCheckerRSCParam(object):
continues up until max_level is
reached (even if sat found)
"""
if not isinstance(formulae_list, (list, tuple)):
print_error("Expected a list of formulae")
self.reset()
print("[" + colour_str(C_BOLD, "i") +
"] Running rsLTL bounded model checking")
print("[" + colour_str(C_BOLD, "i") + "] Formula: " + str(formula))
num_of_paths = len(formulae_list)
# formula = formulae[0]
print_info("Running rsLTL bounded model checking")
print_info("Tested formulae:")
for form in formulae_list:
print_info(" "*4 + str(form))
if print_time:
# start = time()
start = resource.getrusage(resource.RUSAGE_SELF).ru_utime
self.prepare_all_variables()
self.solver_add(self.enc_init_state(0))
self.prepare_all_variables(num_of_paths)
self.load_varset_for_path(0)
# initial states for all the paths
initial_states = []
for path_idx in range(num_of_paths):
initial_states.append(self.enc_init_state(0, path_idx))
self.solver_add(initial_states)
self.current_level = 0
self.prepare_all_variables()
self.prepare_all_variables(num_of_paths)
self.solver_add(self.enc_concentration_levels_assertion(0))
self.solver_add(self.enc_param_concentration_levels_assertion())
# assertions for all the paths and parameters
additional_assertions = []
for path_idx in range(num_of_paths):
additional_assertions.append(self.enc_concentration_levels_assertion(0, path_idx))
additional_assertions.append(self.enc_param_concentration_levels_assertion())
self.solver_add(additional_assertions)
if self.optimise:
self.assert_param_optimisation()
encoder = rsLTL_Encoder(self)
print_info("Iterating...")
while True:
self.prepare_all_variables()
self.solver_add(
self.enc_concentration_levels_assertion(
self.current_level + 1))
print(
"\n{:-^70}".format("[ Working at level=" + str(self.current_level) + " ]"))
stdout.flush()
# stdout.flush()
# reachability test:
self.solver.push()
print("[" + colour_str(C_BOLD, "i") +
"] Generating the formula encoding...")
enc_form = []
for formula in formulae_list:
path_idx = formulae_list.index(formula)
print_info("Generating the encoding for {:s} ({:d} of {:d})".format(
str(formula), path_idx+1, len(formulae_list)))
f = encoder.get_encoding(formula, self.current_level)
ncalls = encoder.get_ncalls()
encoder.load_variables(
var_rs=self.path_v[path_idx],
var_ctx=self.path_v_ctx[path_idx],
var_loop_pos=self.path_loop_position[path_idx])
enc_form.append(encoder.get_encoding(formula, self.current_level))
ncalls = encoder.get_ncalls()
print("[" + colour_str(C_BOLD, "i") + "] Cache hits: " +
str(encoder.get_cache_hits()) + ", encode calls: " +
str(ncalls[0]) + " (approx: " + str(ncalls[1]) + ")")
print("[" + colour_str(C_BOLD, "i") +
"] Adding the formula to the solver...")
print_info("Cache hits: {:d}, encode calls: {:d} (approx: {:d})".format(
encoder.get_cache_hits(), ncalls[0], ncalls[1]))
encoder.flush_cache()
self.solver_add(f)
encoder.flush_cache()
print_info("Adding the formulae to the solver...")
# print (enc_form)
self.solver_add(enc_form)
print("[" + colour_str(C_BOLD, "i") +
"] Adding the loops encoding...")
print_info("Adding the loops encoding...")
self.solver_add(self.get_loop_encodings())
print_info("Testing satisfiability...")
result = self.solver.check()
if result == sat:
print(
"[" + colour_str(C_BOLD, "+") + "] " +
colour_str(
C_GREEN, "SAT at level=" + str(self.current_level)))
print(self.solver.model())
print_positive(green_str(
"SAT at level={:d}".format(self.current_level)))
# print(self.solver.model())
if print_witness:
print("\n{:=^70}".format("[ WITNESS ]"))
self.decode_witness(self.current_level)
for formula in formulae_list:
path_idx = formulae_list.index(formula)
print("\n{:=^70}".format("[ WITNESS ]"))
print("\n Witness for: {:s}".format(str(formula)))
self.decode_witness(self.current_level, path_idx)
if not cont_if_sat:
break
else:
print_info("Unsat")
self.solver.pop()
print("[" + colour_str(C_BOLD, "i") +
"] Unrolling the transition relation")
self.solver_add(self.enc_transition_relation(self.current_level))
self.prepare_all_variables(num_of_paths)
# assertions for all the paths
additional_assertions = []
for path_idx in range(num_of_paths):
additional_assertions.append(
self.enc_concentration_levels_assertion(self.current_level + 1, path_idx))
self.solver_add(additional_assertions)
print_info("Unrolling the transition relation")
for path_idx in range(num_of_paths):
self.solver_add(self.enc_transition_relation(self.current_level, path_idx))
print(
"{:->70}".format("[ level=" + str(self.current_level) + " done ]"))